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Submarine groundwater discharge (SGD) was quantified at select sites in San Francisco Bay (SFB) from radium (223Ra and 224Ra) and radon (222Rn) activities measured in groundwater and surface water using simple mass balance box models. Based on these models, discharge rates in South and Central Bays were 0.3–7.4 m3 day−1 m−1. Although SGD fluxes at the two regions (Central and South Bays) of SFB were of the same order of magnitude, the dissolved inorganic nitrogen (DIN) species associated with SGD were different. In the South Bay, ammonium (NH 4 + ) concentrations in groundwater were three-fold higher than in open bay waters, and NH 4 + was the primary DIN form discharged by SGD. At the Central Bay site, the primary DIN form in groundwater and associated discharge was nitrate (NO 3 − ). The stable isotope signatures (δ15NNO3 and δ18ONO3) of NO 3 − in the South Bay groundwater and surface waters were both consistent with NO 3 − derived from NH 4 + that was isotopically enriched in 15N by NH 4 + volatilization. Based on the calculated SGD fluxes and groundwater nutrient concentrations, nutrient fluxes associated with SGD can account for up to 16 % of DIN and 22 % of DIP in South and Central Bays. The form of DIN contributed to surface waters from SGD may impact the ratio of NO 3 − to NH 4 + available to phytoplankton with implications to bay productivity, phytoplankton species distribution, and nutrient uptake rates. This assessment of nutrient delivery via groundwater discharge in SFB may provide vital information for future bay ecological wellbeing and sensitivity to future environmental stressors.